Bodily zoo US scientists have analysed samples taken from swabs and scrapings to develop the first genetic reference map of nearly all of the microbes inhabiting healthy humans.

Like the mapping of the human genome more than a decade ago, this five-year, US$173 million census of the microbes - including bacteria, viruses and fungi - that inhabit healthy humans will be used as a reference by scientists the world over as they carry out research on human disease.

Researchers sampled up to 18 sites on participants' bodies and looked at everything from saliva to blood, skin and stool.

"This is a whole new way of looking at human biology and human disease, and it's awe-inspiring. It offers incredible new opportunities," says Dr Phillip Tarr of Washington University School of Medicine in St. Louis, who was one of 200 US scientists who took part in the effort, known as the Human Microbiome Project.

Sharing our bodies

Physicians and researchers have long known that humans share their bodies with trillions of microorganisms, says Dr Eric Green, director of the National Human Genome Research Institute, one of the National Institutes of Health that backed the research.

Prior estimates suggest there are 10 bacterial cells for every single human cell in the body, but because they are so small, microbial cells make up just 1 to 3 per cent of our bodies' mass. In a 90 kilogram adult, that is 1 to 3 kilograms of bacteria, says Green.

"Most of the time, humans live in harmony with our microbial hosts, but sometimes that harmony breaks down, resulting in disease," says Green.

Understanding what makes up a normal microbiome will help doctors better understand the changes that occur when people become sick, he says.

Presented in two papers in the journal Nature and 12 papers in the journal PLoS One, the researchers found that humans play host to as many as 10,000 different microbial species.

Some of the microbes found in healthy people are known to cause nasty illnesses, yet they were peacefully coexisting with an abundance of other beneficial microorganisms in this newly defined human microbiome.

New way of thinking

Scientists say this new reference database of microbes in healthy humans will change the way doctors think about infections, moving from a model of one germ causing disease, to thinking about factors that alter the healthy ecosystem of microbes living in people.

Prior to this study, scientists would culture microbes in lab dishes, but many of the microbes that live in humans are difficult to culture this way, and so far, only a few hundred species have been isolated in the human body.

Instead of trying to grow cultures, researchers sampled as many as 18 different sites targeting five main body areas, including the airways, the skin, the mouth, the digestive tract and the vagina.

These samples were donated from 242 healthy people ranging in age from 18 to 40 living near Houston or St Louis.

The researchers then purified all of the DNA in the sample, sequenced the genes and used high-powered computer programs to analyse the data and identify which microbes were present in different areas of the body and in what amounts.

"The beauty of this approach is it identifies everything that is there, giving us complete views of the microbiome at a given body site, like an explorer mapping the coastline of a newly discovered continent for the very first time," says Green.